8B6U | pdb_00008b6u

Mpf2Ba1 monomer

• PDB DOI: https://doi.org/10.2210/pdb8B6U/pdb

• Classification: TOXIN
• Organism(s): Pseudomonas monteilii
• Mutation(s): No 


• Deposited: 2022-09-27 Released: 2023-05-31 
• Deposition Author(s): Marini, G., Poland, B., Leininger, C., Lukoyanova, N., Spielbauer, D., Barry, J., Altier, D., Lum, A., Scolaro, E., Perez-Ortega, C., Yalpani, N., Sandahl, G., Mabry, T., Klever, J., Nowatzki, T., Zhao, J.Z., Sethi, A., Kassa, A., Crane, V., Lu, A., Nelson, M.E., Eswar, N., Topf, M., Saibil, H.R.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.208 (DCC) 

Starting Model: experimental

Literature

Structural journey of an insecticidal protein against western corn rootworm.

Marini, G., Poland, B., Leininger, C., Lukoyanova, N., Spielbauer, D., Barry, J.K., Altier, D., Lum, A., Scolaro, E., Ortega, C.P., Yalpani, N., Sandahl, G., Mabry, T., Klever, J., Nowatzki, T., Zhao, J.Z., Sethi, A., Kassa, A., Crane, V., Lu, A.L., Nelson, M.E., Eswar, N., Topf, M., Saibil, H.R.

(2023) Nat Commun 14: 4171-4171

• PubMed: 37443175 
• DOI: https://doi.org/10.1038/s41467-023-39891-7
• Primary Citation Related Structures: 
  8B6U, 8B6V, 8B6W


• PubMed Abstract: 
  

  The broad adoption of transgenic crops has revolutionized agriculture. However, resistance to insecticidal proteins by agricultural pests poses a continuous challenge to maintaining crop productivity and new proteins are urgently needed to replace those utilized for existing transgenic traits. We identified an insecticidal membrane attack complex/perforin (MACPF) protein, Mpf2Ba1, with strong activity against the devastating coleopteran pest western corn rootworm (WCR) and a novel site of action. Using an integrative structural biology approach, we determined monomeric, pre-pore and pore structures, revealing changes between structural states at high resolution. We discovered an assembly inhibition mechanism, a molecular switch that activates pre-pore oligomerization upon gut fluid incubation and solved the highest resolution MACPF pore structure to-date. Our findings demonstrate not only the utility of Mpf2Ba1 in the development of biotechnology solutions for protecting maize from WCR to promote food security, but also uncover previously unknown mechanistic principles of bacterial MACPF assembly.

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Organizational Affiliation: 
• Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London, WC1E 7HX, UK.
Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany.
Corteva Agriscience, Johnston, IA, 50131, USA.
Syngenta, Research Triangle Park, NC, 27709, USA.
Willow Biosciences, 319 N Bernardo Ave #4, Mountain View, CA, 94043, USA.
Hologic, Inc., 250 Campus Drive, Marlborough, MA, 01752, USA.
Dept. of Biology, University of British Columbia Okanagan, 3187 University Way, Kelowna, BC, V1V 1V7, Canada.
Corteva Agriscience, Ivesdale, IL, 61851, USA.
Corteva Agriscience, Johnston, IA, 50131, USA. [e-mail].
Corteva Agriscience, Johnston, IA, 50131, USA. [e-mail].
Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London, WC1E 7HX, UK. [e-mail].
Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany. [e-mail].
Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet St, London, WC1E 7HX, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.22 kDa 
• Atom Count: 3,915 
• Modeled Residue Count: 481 
• Deposited Residue Count: 483 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mpf2Ba1	A	483	Pseudomonas monteilii	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.208 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.6	α = 90
b = 127.6	β = 90
c = 116.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Marini, G., Poland, B., Leininger, C., Lukoyanova, N., Spielbauer, D., Barry, J., Altier, D., Lum, A., Scolaro, E., Perez-Ortega, C., Yalpani, N., Sandahl, G., Mabry, T., Klever, J., Nowatzki, T., Zhao, J.Z., Sethi, A., Kassa, A., Crane, V., Lu, A., Nelson, M.E., Eswar, N., Topf, M., Saibil, H.R.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	202679/Z/16/Z
Wellcome Trust	United Kingdom	206166/Z/17/Z

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description